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After Lore reveals himself to Jean-Luc Picard, Deanna Troi, and Geordi La Forge, the three are confronted by the fact that Data and Lore are now working together. Lore and Data tell Picard that the end of biological life is at hand and the age of completely artificial lifeforms has begun. Lore had apparently found the Borg struggling with the sense of individuality that Hugh had contracted to the Collective. He sees himself and Data as something for the Borg to aspire to and believe in. He has Data take them away.

On the surface, CommanderRiker and Worf head off to search for the captain's team, which is being led to a holding cell by Data and a Borg. Another team led by Lieutenant Powell will take cover and avoid contact with the Borg. Riker thinks they only have a few days until another Federation ship can arrive.

Picard's team discusses with Data his newfound emotions, and Data responds by telling them how his journey towards being Human was "misguided" and that he now sees the true way that things should be. He appears to be certain of what he's doing, but the others are certain he's being controlled. Data takes their combadges and La Forge's VISOR before leaving. As he activates the force field around their cell, he states coldly, "I am not your puppet any more."

On the planet, Data brings La Forge's VISOR to Lore, who then puts it on and jokingly asks, "How do I look?" Data, not understanding, is confused. Lore remarks that Data will have to work on his sense of humor. Lore intends to experiment on La Forge's implants, saying it's needed to prevent further Borg deaths in the experimentation he has apparently been doing on them, unsuccessfully. They are interrupted by Crosis, who brings a disobedient Borg named Goval to Lore because he was not letting Crosis hear his thoughts. Lore convinces him to comply.

La Forge, in the meantime, has been conspiring with Picard and Troi to find a way around the carrier wave that Lore is using to broadcast his emotions to Data. His ethical subroutines could be rebooted using a kedion pulse, it seems, but in the middle of the conversation, Data enters and takes La Forge away for experimentation without even stopping to talk.

Riker and Worf are following the trail of the captain when they are cornered by some Borg, who take them into a cave. Surprisingly, they find Hugh, who is quite angry in seeing them.

Hugh, apparently leader of an underground group of Borg, does not like the return of the crew of the Enterprise, whom he blames for the current state of the rogue Borg. He explains the effect his individuality had on the Collective, that all the Borg's voices became increasingly discordant, leading to dysfunction. They would listen to any voice to end the resulting confusion, and then they encountered Lore, who promised clarity and purpose to the Borg that were not connected to the Collective anymore. He shows Riker and Worf the results of the experiments that Lore is attempting on the Borg, to the end of becoming a superior race: two individuals in an obviously bad state. However, he agrees to show Riker and Worf a way into the compound to save his friend, La Forge.

La Forge, meanwhile, is strapped to a table to undergo an experiment. Data comes in with Picard's voice in an attempt at humor, unsuccessfully. Data explains the procedure of replacing control of his cognitive abilities with an artificial neural network, which has a 60% mortality rate. La Forge explains Lore is manipulating him, but he ignores him.

In the cell, Troi, standing over the body of Picard, calls a Borg over to help her. When the Borg leans over to check out Picard, the Captain pulls out a cable on the Borg's neck. Picard then steals the interlink transceiver while Troi takes the weapon from the Borg's arm to check the hall. There, she finds Data escorting La Forge back to the cell. Data takes the weapon and leaves with the Borg, unaware of the lost transceiver. Picard then begins to modify it to help activate Data's ethical subroutines, with La Forge's guidance.

The Enterprise drops out of warp and transporter chiefSalazar transports the last of the crew off of the surface, but informs the bridge that six people (Picard, Riker, Troi, Worf, La Forge, and an officer who had been killed by the Borg) still remain. Just as the Borg ship returns for another fight, Crusher orders shields up, but the Enterprise takes a hit which disables their warp drive. Retaliating with phasers, the Borg ship fires again which takes a toll on the shields. Crusher then orders the Enterprise into the nearby sun's corona, much to Taitt's disbelief.

Approaching the star, Crusher orders Barnaby to activate the metaphasic shielding, but he reminds her that the shield is still in an experimental stage. Once activated, it works; it lowers the radiation level and temperature of the hull while getting the Borg ship off their tail. The Borg take a position, letting them know that they will wait until they come out of the sun. Crusher wonders how long they can stay in the sun's corona.

Picard has finished modifications on the interlink transceiver, and places it near the force field, activating the pulse that will reset Data's subroutines. Meanwhile, Data is ready to irradiate La Forge's braincells and begin construction of a positronic net to take the place of his biological brain. However, the pulse works, and at La Forge's coaxing, Data thinks of a false excuse to not destroy La Forge's brain yet.

Outside, Lore and Data are chatting regarding La Forge. Data then projects accountability towards his comrades, stating that if they die, he is responsible. Lore wonders if something is wrong with Data's systems, then begins to induce pain within Data. Under duress, Data asks for more emotions, which Lore gives. As soon as he leaves, Crosis emerges and Lore wonders if Data has the strength to help Lore in his plan.

Faced with only a few minutes of metaphasic shielding left, Taitt, having done her senior honors thesis on solar dynamics at the Academy, thinks up a plan to create a solar eruption to destroy the Borg ship. Barnaby objects, reminding Taitt that this is not the Academy, and that comparing the two is a long way from actually trying it. Taitt assures him that she's got a targeting sequence lined up. Barnaby tells her if her calculations are even slightly off, the eruption could obliterate the Enterprise as well. Taitt bluntly reassures him, echoing his own retort from earlier. After firing phasers and using the tractor beam, the Borg ship is destroyed, to the surprise and delight of Barnaby. Taitt just gives him a sly grin. With the Borg ship destroyed, the Enterprise is free to orbit the planet again.

Back on the planet, Data returns with La Forge and then takes Picard, who begins to confuse Data by activating portions of his ethical subroutines. Lore interrupts them, and, as part of a ceremony, orders Data to kill Picard. The ethical subroutine has been activated, and Data tells Lore that that would be wrong. Beneath the surface, Riker and Worf use the environmental conduits to get to the central room, and then attack at a key point in the events when Lore was about to kill Data. Hugh tackles Lore, preventing him from killing Data. The Borg fight back and amongst themselves. In the chaos that ensues, Lore escapes from the room, and Data follows. As Lore tries to coerce Data into leaving the planet with him, Data shoots and proceeds to deactivate his brother once and for all. Lore's last words before his deactivation are, "I love you, brother."

Picard, Riker, and Worf thank Hugh and welcome Data back to normal functioning. Picard hints that even though Hugh is unsure of their future, perhaps these Borg have a good individual leader for the future.

Back on the ship, La Forge enters Data's quarters and walks over to his desk, where Spot is lying. La Forge tells Data that he will return to duty soon. Data is relieved at this, and shows La Forge the damaged and inoperative emotion chip that was retrieved from Lore's body. He is about to destroy it with a phaser, because his friendship with La Forge is more important to him than emotions, and emotions are what caused him to harm and nearly kill his friend. La Forge stops him and says that perhaps someday they will be able to use the emotion chip. After all, it is Data's lifelong dream to have emotions, and, as La Forge concludes, "I wouldn't be very much of a friend if I let you give up on a life-long dream now, would I? Maybe some day, when you're ready."

"They had lost their sense of purpose. Well, I gave them their purpose... and they gave me mine."

- Lore, on the Borg he discovered and later became leader of

"The reign of biological life-forms is coming to an end. You, Picard, and those like you, are obsolete!"

- Lore

"Give me your VISOR."
"Why?"
"Give it to me... or I will take it by force!"

- Data and La Forge

"I now realize that my life aboard the Enterprise was a waste. My quest to become Human, misguided. An evolutionary step in the wrong direction .... I am not your puppet anymore!"

- Data, under Lore's influence

"What's your name?"
"Taitt, sir."
"I don't think I've seen you before."
"I was just posted here six weeks ago."
"Well, Taitt, I bet you never thought you'd be serving as Tactical Officer after only six weeks."
"No, sir, I sure didn't!"

Interiors of the compound were a narrow three-wall set that was multiplied optically, along with the Borg extras. These were left standing over hiatus, but the caverns were built for this episode. (Star Trek: The Next Generation Companion)

The terminal that Lore is working at just prior to his deactivation is the same prop as the theta-band wave emitter in "Chain of Command, Part I".

Jonathan Del Arco reprises his role as Hugh from the TNG's fifth season episode "I Borg". However, he shares no screen time with Geordi, with whom he had the closest relationship in the earlier episode, although their friendship is mentioned.

At the end of the season, it is implied that Data would eventually begin to use the emotion chip, as shown in the alternate future timeline of "All Good Things..." in which he remarks that his housekeeper makes him laugh. The emotion chip was next seen in Star Trek Generations, where it became fused into Data's neural net, forcing him to learn to deal with having emotions on a permanent basis. He eventually gains the ability to deactivate, and later remove completely, the chip in Star Trek: First Contact and Star Trek: Insurrection. The design of the emotion chip seen here is different than the one seen in Star Trek Generations.

Geordi mentions that, while attempting to swim at Devala Lake, Data sunk to the bottom, though in Star Trek: Insurrection, it is shown that Data has been designed to act as a flotation device.